Related papers: Automatic annotation of bioinformatics workflows w…
Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…
Ever-expanding volumes of biomedical text require automated semantic annotation techniques to curate and put to best use. An established field of research seeks to link mentions in text to knowledge bases such as those included in the UMLS…
SMCalFlow is a large corpus of semantically detailed annotations of task-oriented natural dialogues. The annotations use a dataflow approach, in which the annotations are programs which represent user requests. Despite the availability,…
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for…
This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts…
The annotation of textual information is a fundamental activity in Linguistics and Computational Linguistics. This article presents various observations on annotations. It approaches the topic from several angles including Hypertext,…
Properly annotated multimedia content is crucial for supporting advances in many Information Retrieval applications. It enables, for instance, the development of automatic tools for the annotation of large and diverse multimedia…
Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain,in particular about the available services and their behavior in terms of input/output data descriptions. In…
Modern problems of concept annotation associate an object of interest (gene, individual, text document) with a set of interrelated textual descriptors (functions, diseases, topics), often organized in concept hierarchies or ontologies. Most…
This technical report presents an evaluation of the ontology annotations in the metadata of a subset of entries of MetaboLights, a database for Metabolomics experiments and derived information. The work includes a manual analysis of the…
Ontologies present an attractive technology for describing bio-medicine, because they can be shared, and have rich computational properties. However, they lack the rich expressivity of English and fit poorly with the current scientific…
The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this…
Manually annotated data is key to developing text-mining and information-extraction algorithms. However, human annotation requires considerable time, effort and expertise. Given the rapid growth of biomedical literature, it is paramount to…
We present an ontology for representing workflows over components with Read-Write Linked Data interfaces and give an operational semantics to the ontology via a rule language. Workflow languages have been successfully applied for modelling…
Many recent works aim at developing methods and tools for the processing of semantic Web services. In order to be properly tested, these tools must be applied to an appropriate benchmark, taking the form of a collection of semantic WS…
Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…
Successful management of emotional stimuli is a pivotal issue concerning Affective Computing (AC) and the related research. As a subfield of Artificial Intelligence, AC is concerned not only with the design of computer systems and the…
An advantage of scientific workflow systems is their ability to collect runtime provenance information as an execution trace. Traces include the computation steps invoked as part of the workflow run along with the corresponding data…
Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language process (BioNLP) projects attempt to address this challenge, but the state of the art in…
Creating linguistic annotations requires more than just a reliable annotation scheme. Annotation can be a complex endeavour potentially involving many people, stages, and tools. This chapter outlines the process of creating end-to-end…